Synonymous and nonsynonymous distances help untangle convergent evolution and recombination.

ABSTRACT: When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because different segments of the sequence alignment support different phylogenies. Similarly, convergent selective pressures at the molecular level can also lead to phylogenetic tree incongruence across the sequence alignment. Current methods for detection of phylogenetic incongruence are not equipped to distinguish between these two different mechanisms and assume that the incongruence is a result of recombination or other horizontal transfer of genetic information. We propose a new recombination detection method that can make this distinction, based on synonymous cod

SUBMITTER: Chi PB 

PROVIDER: S-EPMC4521982 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature